rs7940107

Variant names:

• chr11-69260303-G-A
• rs7940107

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.198 in 152,036 control chromosomes in the GnomAD database, including 3,590 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (3590 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30020 AN: 151918 Hom.: 3577 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0118

Gnomad SAS AF: 0.0448

Gnomad FIN AF: 0.0665

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.212

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.198 AC: 30066 AN: 152036 Hom.: 3590 Cov.: 32 AF XY: 0.187 AC XY: 13893 AN XY: 74306

African (AFR) AF: 0.321 AC: 13297 AN: 41460

American (AMR) AF: 0.154 AC: 2351 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 785 AN: 3466

East Asian (EAS) AF: 0.0120 AC: 62 AN: 5170

South Asian (SAS) AF: 0.0438 AC: 211 AN: 4814

European-Finnish (FIN) AF: 0.0665 AC: 703 AN: 10574

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12024 AN: 67966

Other (OTH) AF: 0.212 AC: 447 AN: 2110

Alfa AF: 0.186 Hom.: 4476

Bravo AF: 0.213

Asia WGS AF: 0.0660 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.79
DANN	Benign	0.54
PhyloP100		-0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7940107; hg19: chr11-69027770;